Yes, it was my initial thought that it should work fine since they were two separate libraries. I wanted to use libaacplus for 64k SBR and 32k SBR+PS; and use libvo_aacenc for 128 and 256 kbps. Instead of libvo I'm using faac (quality isn't noticeable issue). Also SBR and PS don't work at all for libvo... are they supposed to?

That might easily depend on things like default visibility, whether -Bsymbols was used in linking etc.
If those are distribution builds they may just have done a better job of packaging them, or they are later versions that fixed the issue.